The waterbased paint is still wet? I have never encountered that.
The first time that I encountered MS polymers such as CT1, they had been used by the sash window restorer. I applied oil based paint directly over it- it stayed tacky for days. I hit it with a coat of waterbased undercoat and it was fine the next day.
Another job, I used CT1 to fill the gaps between a customer's floor and skirting. A year later I went back to decorate. I had forgotten that I had used CT1 and applied a coat of oil based eggshell to the skirting. It stayed tacky until I hit it with waterbased paint.
I recently come across a team of decorators that tried to paint over CT1 a couple of hours after applying it. They used waterbased paints. The paint dried, but crazed. I did try explaining that they need to wait until the next day, but it got lost in translation.